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- PDB-6jhi: Crystal structure of mutant D470A of Pullulanase from Paenibacill... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6jhi | ||||||||||||
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Title | Crystal structure of mutant D470A of Pullulanase from Paenibacillus barengoltzii complexed with maltotetraose | ||||||||||||
![]() | Pulullanase | ||||||||||||
![]() | HYDROLASE / GH13 / Pullulanase / maltotetraose | ||||||||||||
Function / homology | ![]() pullulanase / pullulanase activity / carbohydrate metabolic process / metal ion binding Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Wu, S.W. / Yang, S.Q. / Qin, Z. / You, X. / Huang, P. / Jiang, Z.Q. | ||||||||||||
![]() | ![]() Title: Crystal structure of mutant D470A of Pullulanase from Paenibacillus barengoltzii complexed with maltotetraose Authors: Wu, S.W. / Yang, S.Q. / Qin, Z. / You, X. / Huang, P. / Jiang, Z.Q. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 153.5 KB | Display | ![]() |
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PDB format | ![]() | 115.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2e8yS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 75139.602 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Residues 1-8 (MLSVQKEF) and 638-658(GASGEAAAAAPAAAGGPPAGG) had low-level electron density and were not included in the model. Source: (gene. exp.) ![]() Production host: ![]() ![]() References: UniProt: A0A0C5GWS2, pullulanase | ||||||
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#2: Polysaccharide | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.87 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.08M calcium chloride, 0.1M MES, 22% PEG 3350, 0.7% beta-OG, pH 6.5 Temp details: 291-295 |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: 90-100 / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 25, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97776 Å / Relative weight: 1 |
Reflection | Resolution: 2.319→50 Å / Num. obs: 30977 / % possible obs: 98.5 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.113 / Net I/σ(I): 14.742 |
Reflection shell | Resolution: 2.319→2.36 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.226 / Mean I/σ(I) obs: 7.778 / Num. unique obs: 1622 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2E8Y Resolution: 2.319→38.068 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.07 Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.319→38.068 Å
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Refine LS restraints |
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LS refinement shell |
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